Bruce and Frank, Thank you for looking into this. Please let me know if there is any more information I can provide that would be helpful in identifying the problem. Regards, Ellen On Fri, Oct 3, 2014 at 1:15 PM, Schima, Frank wrote:

Hi all,

While I’m unsure what PCA is, PDL and PDL::Stats are available and installed with Demeter(-devel) in Macports.

$ port installed | grep pdl p5.16-pdl @2.7.0_5 (active) p5.16-pdl-stats @0.6.5_0 (active)

I don’t have an explanation for what the problem might be. I won’t be able to look into this until Monday at the earliest.

Cheers! Frank

On Oct 3, 2014, at 1:01 PM, Bruce Ravel wrote:

Ellen,

There is no a priori reason that PCA should not be available. That said, Athena is careful to fail gracefully (i.e. with that message displayed) when it fails to find the bits that make PCA happen.

My guess is it's a packaging issue on MacPorts. Let's ask Frank!

Frank,

Are PDL and PDL::Stats dependencies for the Demeter package on MacPorts?

A quick perusal of the available ports at macports.org suggests that there may not be a package for PDL::Stats for the version of Perl you are using. That seems rectifiable....

Thanks, B

On 10/03/2014 02:50 PM, Ellen Daugherty wrote:

Hello XAFS community,

I recently upgraded to the new version of Demeter (0.9.20) for Mac and am trying to run principal components analysis on my spectra. When I click on "Principle components analysis" from the main menu, the window shows the following message: "PCA is not enabled on this computer. The most likely reason is that the perl modules PDL and/or PDL::Stats are not available."

Perhaps the solution here is simple, but I am not familiar with perl modules and do not understand the source of the issue. I could not find information about this problem in the Mail Archive, though I may have missed something. Do I need to download the PDL perl modules separately from the Demeter installation? Could there be files that are not located in the proper directory? Or perhaps PCA is simply not available for Macs?

Please let me know if further information would help in solving this problem.

Thank you!

Ellen

-- Graduate Student Research Assistant Department of Chemistry Colorado State University

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Ph.D. Candidate Research Assistant Department of Chemistry Colorado State University

On 10/07/2014 02:43 PM, Schima, Frank wrote:

I’m going to need specific steps to reproduce the issue.

As I understood the issue from Ellen's first message, the problem is that Athena is not able to find the modules "PDL::Lite" (which should be installed when "PDL" is installed) and/or "PDL::Stats::GLM". If I force Athena to fail to load one of them, then selecting "Principle Components Analysis" from the main menu will look like the first attachment. If Athena can find those two modules, the selecting "Principle Components Analysis" will look like the second attachment. The test in Athena is really simple. If those two modules can be loaded successfully, then the PCA tool will display properly. If not, that message is the graceful fall back. My guess is that one or both of those perl modules is not being found on Ellen's computer. A simple way to test from the command line whether the modules can be loaded is to do perl -e 'use PDL::Lite' or perl -e 'use PDL::Stats::GLM' If they cannot be found, then perl spits up an error message. If they can, then nothing happens. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

Bruce and Frank, In response to Bruce's suggestion: A simple way to test from the command line whether the modules can be loaded is to do perl -e 'use PDL::Lite' My output is: "Can't locate PDL/Lite.pm in @INC (@INC contains: /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at -e line 1. BEGIN failed--compilation aborted at -e line 1." In response to Frank's suggestions: $ port installed perl5 My output is: -bash: port: command not found And for, $ echo $PATH My output is: /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin Does this mean that there is a problem with the Macports location? Thank you! Ellen On Tue, Oct 7, 2014 at 2:18 PM, Schima, Frank wrote:

On Oct 7, 2014, at 1:29 PM, Bruce Ravel wrote:

On 10/07/2014 02:43 PM, Schima, Frank wrote:

I’m going to need specific steps to reproduce the issue.

As I understood the issue from Ellen's first message, the problem is that Athena is not able to find the modules "PDL::Lite" (which should be installed when "PDL" is installed) and/or "PDL::Stats::GLM".

If I force Athena to fail to load one of them, then selecting "Principle Components Analysis" from the main menu will look like the first attachment.

If Athena can find those two modules, the selecting "Principle Components Analysis" will look like the second attachment.

The test in Athena is really simple. If those two modules can be loaded successfully, then the PCA tool will display properly. If not, that message is the graceful fall back. My guess is that one or both of those perl modules is not being found on Ellen's computer.

A simple way to test from the command line whether the modules can be loaded is to do

perl -e 'use PDL::Lite' or perl -e 'use PDL::Stats::GLM'

If they cannot be found, then perl spits up an error message. If they can, then nothing happens.

Nothing happens for me. So they are installed. At this point it looks like an issue with her Macports install.

I would start by verifying that she is correctly using perl 5.16 in Macports. What is the output of the following?

$ port installed perl5

Here is my output.

The following ports are currently installed: perl5 @5.12.4_0+perl5_16 (active)

Then the Macports perl needs to be in your path. What is the output of the following?

$ echo $PATH

My output is:

/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

Cheers! Frank

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Frank, I apologize for not responding sooner, other urgent issues suddenly came up! I followed Bruce's installation directions on the Demeter page ( http://bruceravel.github.io/demeter/) and the Xcode ( https://guide.macports.org/#installing.xcode) and Macports ( https://www.macports.org/install.php) installation instructions. I had issues the first time I tried to install Demeter (i.e. text in Terminal indicated things weren't proceeding successfully and it was taking a long time), but the second time, it appeared to work. I now am receiving the "command not found" response when trying to open the Athena program in Terminal. I don't know why that didn't happen earlier. Ellen On Wed, Oct 8, 2014 at 3:55 PM, Schima, Frank wrote:

On Oct 7, 2014, at 5:08 PM, Ellen Daugherty wrote:

Bruce and Frank,

In response to Bruce's suggestion:

A simple way to test from the command line whether the modules can be loaded is to do

perl -e 'use PDL::Lite'

My output is:

"Can't locate PDL/Lite.pm in @INC (@INC contains: /Library/Perl/5.16/darwin-thread-multi-2level /Library/Perl/5.16 /Network/Library/Perl/5.16/darwin-thread-multi-2level /Network/Library/Perl/5.16 /Library/Perl/Updates/5.16.2 /System/Library/Perl/5.16/darwin-thread-multi-2level /System/Library/Perl/5.16 /System/Library/Perl/Extras/5.16/darwin-thread-multi-2level /System/Library/Perl/Extras/5.16 .) at -e line 1.

BEGIN failed--compilation aborted at -e line 1."

In response to Frank's suggestions:

$ port installed perl5

My output is:

-bash: port: command not found

And for,

$ echo $PATH

My output is:

/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

Does this mean that there is a problem with the Macports location?

It means your path is not setup to find Macports. It says nothing about if Macports is installed or not. So when you run “perl” you are using the OS X perl and of course that won’t work. Now I’m really curious. Given this, how did you install the demeter-devel port and how are you actually running demeter programs? You would have encountered the same “command not found “ errors unless your path was correct like mine is.

-Frank

Thank you!

Ellen

On Tue, Oct 7, 2014 at 2:18 PM, Schima, Frank wrote:

...

On Oct 7, 2014, at 1:29 PM, Bruce Ravel wrote:

On 10/07/2014 02:43 PM, Schima, Frank wrote:

I’m going to need specific steps to reproduce the issue.

As I understood the issue from Ellen's first message, the problem is that Athena is not able to find the modules "PDL::Lite" (which should be installed when "PDL" is installed) and/or "PDL::Stats::GLM".

If I force Athena to fail to load one of them, then selecting "Principle Components Analysis" from the main menu will look like the first attachment.

If Athena can find those two modules, the selecting "Principle Components Analysis" will look like the second attachment.

The test in Athena is really simple. If those two modules can be loaded successfully, then the PCA tool will display properly. If not, that message is the graceful fall back. My guess is that one or both of those perl modules is not being found on Ellen's computer.

A simple way to test from the command line whether the modules can be loaded is to do

perl -e 'use PDL::Lite' or perl -e 'use PDL::Stats::GLM'

If they cannot be found, then perl spits up an error message. If they can, then nothing happens.

Nothing happens for me. So they are installed. At this point it looks like an issue with her Macports install.

I would start by verifying that she is correctly using perl 5.16 in Macports. What is the output of the following?

$ port installed perl5

Here is my output.

The following ports are currently installed: perl5 @5.12.4_0+perl5_16 (active)

Then the Macports perl needs to be in your path. What is the output of the following?

$ echo $PATH

My output is:

/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin

Cheers! Frank

B

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Should it matter that I still have the old iXAFS program loaded on my computer? This package is still fully functional. I am wondering if I need to wipe out all the material I downloaded in order to install Demeter (including MacPorts) and reinstall. I have the same OS as Paul, so I don't think that this is an OS problem. Thanks! Ellen On Tue, Oct 7, 2014 at 9:00 PM, Paul Fons wrote:

I just wanted to add the comment "works here" for @0.9.20pre10. This is probably more helpful to Frank than Ellen, but it would seem that it something unique to Ellen's configuration. I am running Mavericks 10.9.5 by the way.

Cheers, Paul On Oct 4, 2014, at 3:50, Ellen Daugherty wrote:

Hello XAFS community,

I recently upgraded to the new version of Demeter (0.9.20) for Mac and am trying to run principal components analysis on my spectra. When I click on "Principle components analysis" from the main menu, the window shows the following message: "PCA is not enabled on this computer. The most likely reason is that the perl modules PDL and/or PDL::Stats are not available."

Perhaps the solution here is simple, but I am not familiar with perl modules and do not understand the source of the issue. I could not find information about this problem in the Mail Archive, though I may have missed something. Do I need to download the PDL perl modules separately from the Demeter installation? Could there be files that are not located in the proper directory? Or perhaps PCA is simply not available for Macs?

Please let me know if further information would help in solving this problem.

Thank you!

Ellen

-- Graduate Student Research Assistant Department of Chemistry Colorado State University _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Ph.D. Candidate Research Assistant Department of Chemistry Colorado State University